Elevated levels of serum gamma-glutamyltransferase (GGT) levels have been found to predict the development of type 2 diabetes in adults. The role of GGT in insulin resistance (IR) among children is largely unknown. We investigated whether GGT among hepatic enzymes is independently associated with IR in obese Korean children. A total of 1308 overweight (above the 85th BMI percentile of Korean reference) boys (n = 822) and girls (n = 486), aged 9-15 years, were studied. Measures acquired included weight, height, percent body fat (BF%), waist circumference, blood pressure, blood glucose and insulin, C-reactive protein, total cholesterol, triglycerides, HDL-Cholesterol, GGT, aspartate aminotransferase (AST), and alanine aminotransferase (ALT). IR was calculated using the homeostasis model assessment (HOMA-IR). Serum GGT and ALT, but not AST, were positively correlated with HOMA-IR in boys (r = 0.222 for GGT; P < 0.05, r = 0.188 for ALT; P < 0.05) and girls (r = 0.292 for GGT; P < 0.05, r = 0.258 for ALT; P < 0.05). In multiple regression analysis for HOMA-IR as dependent variable, GGT (β = 0.068; P = 0.053 in boys, β = 0.145; P = 0.002 in girls) and ALT (β = 0.074; P = 0.034 in boys, β = 0.130; P = 0.005 in girls) emerged as determinants of HOMA-IR after adjusting age, BMI, tanner stage, and triglycerides. Serum GGT level is a strong marker of IR in obese Korean children.